Contacts of the helix formed by residues 565 - 575 (chain A) in PDB entry 2OZO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 565 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A VAL* 5.3 11.4 - - + -
533A LEU* 5.3 1.3 - - + -
563A GLU* 3.7 8.7 - - - +
564A CYS* 1.3 91.6 - - - +
566A PRO* 1.3 70.2 - - + +
567A GLU* 3.1 24.9 - - - +
568A LEU* 3.3 36.5 + - + -
569A TYR* 3.4 15.6 + - - +
600A LEU* 4.6 18.2 - - + -
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Residues in contact with PRO 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A CYS 3.6 2.2 - - - +
565A PRO* 1.3 80.8 - - + +
567A GLU* 1.3 71.4 + - + +
569A TYR* 3.2 7.4 + - + +
570A ALA* 2.7 37.9 + - - +
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Residues in contact with GLU 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565A PRO* 3.1 25.2 - - - +
566A PRO* 1.3 103.7 - - + +
568A LEU* 1.3 61.9 + - - +
570A ALA* 3.3 8.4 - - - +
571A LEU* 2.9 27.0 + - - +
592A ARG* 4.9 1.7 + - - -
596A CYS* 3.6 29.6 - - - +
599A SER* 5.4 2.3 + - - -
600A LEU* 5.0 8.1 - - - +
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Residues in contact with LEU 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A VAL* 6.4 0.4 - - + -
439A ALA* 5.1 5.8 - - + -
442A LEU* 5.6 0.2 - - + -
529A MET* 3.4 7.8 - - + +
533A LEU* 3.6 42.0 - - + -
564A CYS* 4.0 0.4 - - - -
565A PRO* 3.3 35.0 - - + +
566A PRO 3.2 0.8 - - - -
567A GLU* 1.3 72.3 - - - +
569A TYR* 1.3 57.0 + - - +
570A ALA 3.0 1.3 - - - -
571A LEU* 3.0 2.8 + - + +
572A MET* 2.6 36.9 + - - +
593A MET* 3.3 29.4 - - + -
596A CYS* 3.7 28.5 - - + -
600A LEU* 4.6 12.8 - - + -
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Residues in contact with TYR 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A ARG* 5.1 4.7 + - - +
558A MET 2.8 24.9 + - - -
559A GLU* 3.6 4.6 - - - -
560A CYS* 3.3 60.3 + - + -
561A PRO* 4.1 2.7 - - + -
564A CYS* 4.1 4.6 - - - -
565A PRO 3.4 5.6 + - - +
566A PRO* 3.2 9.3 + - + +
568A LEU* 1.3 80.2 - - - +
570A ALA* 1.3 53.1 + - - +
572A MET* 3.6 21.8 - - - +
573A SER* 2.7 53.8 + - - -
576A TRP* 4.7 4.5 - + - -
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Residues in contact with ALA 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A PRO 2.7 18.5 + - - +
567A GLU* 3.3 10.8 - - - +
569A TYR* 1.3 80.2 - - - +
571A LEU* 1.3 60.5 + - - +
573A SER* 3.3 7.5 + - - -
574A ASP* 3.0 27.8 + - - +
592A ARG* 4.0 8.5 - - - +
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Residues in contact with LEU 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A MET* 4.0 16.2 - - - -
567A GLU 2.9 14.3 + - - +
568A LEU* 3.4 8.7 - - + +
570A ALA* 1.3 72.5 - - - +
572A MET* 1.3 67.8 + - - +
574A ASP* 3.2 4.8 + - + +
575A CYS* 3.0 25.5 + - - -
584A PRO* 5.7 1.1 - - + -
589A VAL* 4.3 22.9 - - + +
592A ARG* 3.3 52.2 - - + +
593A MET* 3.6 45.5 - - + +
596A CYS* 5.4 2.5 - - - -
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Residues in contact with MET 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A GLY 3.4 18.8 - - - +
529A MET* 3.4 42.8 - - + +
530A TRP* 3.5 27.1 - - + +
533A LEU* 3.6 18.4 - - + -
561A PRO* 4.8 1.6 - - + -
564A CYS* 4.9 2.9 - - - -
568A LEU 2.6 16.2 + - - +
569A TYR* 3.6 21.5 - - + +
571A LEU* 1.3 74.0 - - - +
573A SER* 1.3 57.5 + - - +
575A CYS* 2.9 26.3 + - - +
576A TRP* 3.3 36.1 + - + -
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Residues in contact with SER 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A ARG* 5.8 3.3 - - - +
569A TYR* 2.7 46.5 + - - -
570A ALA* 3.4 8.4 - - - -
571A LEU 3.2 0.2 - - - -
572A MET* 1.3 72.2 - - - +
574A ASP* 1.3 56.5 + - - +
575A CYS 2.9 4.7 - - - -
576A TRP* 2.7 42.6 + - - +
577A ILE* 3.9 4.6 - - - +
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Residues in contact with ASP 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570A ALA* 3.0 10.3 + - - +
571A LEU* 3.2 7.8 + - + +
573A SER* 1.3 81.0 - - - +
575A CYS* 1.3 58.9 + - - +
577A ILE* 2.9 36.1 - - + +
583A ARG* 3.9 1.4 - - - -
584A PRO* 3.3 23.7 - - + +
592A ARG* 2.8 42.1 + - - +
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Residues in contact with CYS 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522A VAL* 3.5 40.6 - - - +
523A TRP* 3.6 11.8 - - - -
525A TYR* 4.3 14.1 - - - -
526A GLY* 3.7 20.2 - - - -
529A MET* 5.0 0.2 - - - -
571A LEU* 3.0 22.0 + - - -
572A MET* 2.9 14.1 + - - +
574A ASP* 1.3 78.1 - - - +
576A TRP* 1.3 62.1 + - - +
577A ILE 3.6 0.4 - - - -
583A ARG* 3.2 17.4 - - - -
584A PRO* 4.8 1.8 - - - -
589A VAL* 4.5 9.9 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il